INVESTIGATING HYPOTHETICAL PRODUCTS FROM NONCODING FRAMES (HYPNOFS)

Hypothetical Products from Noncoding Frames (i.e., HyPNoFs) are hypoth etical, not-coded proteins, translated from alternate reading frames ( i.e., coding+1 and coding+2) of cDNAs. HyPNoFs of CD4, PKC, oncostatin , bcl-2 proto-oncogene, tumor suppressor p53, cystic fibrosis transmem brane regulator (CFTR), and tumor necrosis factors alpha and beta were searched as query sequences vs the SWISS-PROT data bank. Homology sea rches carried out revealed that hypothetical products (i.e., HyPNoFs) may share high similarity with real protein products actually coded. S equence similarity of hypothetical products to real. proteins is somet imes very high, suggesting common conformational features, according t o the Sander and Schneider cutoff value. This finding supports the hyp othesis that eukaryotic DNA, currently considered to be monocistronic, might occasionally have polycistronic regions, carrying different pro tein messages on overlapping frames. As yet, polycistronic genes have been observed in viral genomes only. The presence of polycistronic reg ions in eukaryotic genes is Likely reminiscent of an ancient strategy, rather than a present feature of the genome in eukaryotes. These data suggest that thorough investigation of HyPNoFs is likely to improve o ur ability to trace genes' evolution and to investigate structure-func tion relationships of protein and DNA sequences.